@misc{Walter1989, author = {Walter, Artur}, title = {Ein Finite-Element-Verfahren zur numerischen L{\"o}sung von Erhaltungsgleichungen.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4597}, number = {TR-89-03}, year = {1989}, abstract = {A new approach for the discretisation of hyperbolic conservation laws via a finite element method is developed and analysed. Appropriate forms of the Eulers equation of gas dynamic are considered to employ the algorithm in a reasonable way for this system of nonlinear equations. Both mathematical and physical stability results are obtained. A main part of the paper is devoted to the convergence proof with energy methods under strong regularity of the solution of a scalar nonlinear conservation law. Some hints on the implementation and numerical results for the calculation of transonic gasflow through a Laval nozzle are given. The necessary amount of numerical work is compared to an established finite difference method and the efficiency of the algorithm is shown. A survey on recent literature about finite element methods for hyperbolic problem is included.}, language = {de} } @misc{Deuflhard1989, author = {Deuflhard, Peter}, title = {Numerik von Anfangswertmethoden f{\"u}r gew{\"o}hnliche Differentialgleichungen.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4580}, number = {TR-89-02}, year = {1989}, abstract = {Das voliegende Skriptum entstand aus einer Vorlesung, die ich im WS 87/88 an der Freien Universit{\"a}t Berlin im Fachbereich Mathematik gehalten habe. Mein urspr{\"u}ngliches Vorlesungsmanuskript wurde von Herrn F. Bornemann in weiten Teilen {\"u}berarbeitet, reorganisiert und substantiell erg{\"a}nzt. Der Inhalt stammt gr{\"o}ßtenteils aus Originalarbeiten j{\"u}ngeren Datums. Dar{\"u}berhinaus finden sich zahlreiche Teile, die aus meiner jahrelangen Besch{\"a}ftigung mit dem Thema entstanden aber unpubliziert geblieben sind. Das Skriptum erhebt nicht den Anspruch, ein Lehrbuch zu sein. Es war zun{\"a}chst als Ausarbeitung f{\"u}r meinen studentischen H{\"o}rerkreis sowie als internes Arbeitspapier f{\"u}r das ZIB bestimmt. Die Kunde von der bloßen Existenz eines solchen Skriptums hat jedoch zu einer derart regen Nachfrage gef{\"u}hrt, daß es hiermit als Technischer Report des ZIB einer breiteren ffentlichkeit zug{\"a}nglich gemacht werden soll. In der vorliegenden Form richtet es sich in erster Linie an Mathematiker; es soll sich jedoch auch f{\"u}r Naturwissenschaftler und Ingenieure eignen, die sich einen Einblick in den theoretischen und algorithmischen Hintergrund der von ihnen verwendeten wissenschaftlichen Software verschaffen wollen.}, language = {de} } @misc{OPUS4-457, title = {CRAY-HANDBUCH. Einf{\"u}hrung in die Benutzung der CRAY X-MP unter UNICOS. (veraltet)}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4574}, number = {TR-89-01}, year = {1989}, language = {de} } @misc{MaierhoeferSkorobohatyj1988, author = {Maierh{\"o}fer, Gerhard and Skorobohatyj, Georg}, title = {Parallel-TRAPEX (Ein paralleler adaptiver Algorithmus zur numerischen Integration; seine Implementierung f{\"u}r SUPRENUM-artige Architekturen mit SUSI).}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4560}, number = {TR-88-05}, year = {1988}, abstract = {This paper describes some ways of transforming a sequential adaptive algorithm for numerical evaluation of an integral (Romberg- Quadrature with polynomial Extrapolation method) to a parallel one, such as have been implementad by the authors. We developed an algorithm which preserves the sequential adaptivity and is capable of running on various architectures, dynamically controlling the number of avtive processors depending on the problem. To study the time behaviour, we used the simulator SUSI(SUprenum SImulatur) which is able to simulate SUPRENUM-like architectures. Results are given in part 3. {\bf Keywords:} Romberg quadrature; numerical integration; parallel adaptive algorithm; SUSI; simulation; SUPRENUM; MIMD-Fortran; computer architecture; granularity; load balacing; master-slave-principle.}, language = {de} } @misc{BuhtzLangendorfPaetsch1988, author = {Buhtz, Danuta Anna and Langendorf, Jens and Paetsch, Olaf}, title = {GRAZIL - 3D. Ein graphisches Anwendungsprogramm zur Darstellung von Kurven- und Funktionsverl{\"a}ufen im r{\"a}umlichen Koordinatensystem.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4556}, number = {TR-88-04}, year = {1988}, abstract = {GRAZIL - 3D ist ein interaktives Programmpaket zur graphischen Darstellung von dreidimensionalen Kurvenverl{\"a}ufen. Das Aussehen der r{\"a}umlichen Ausgabe des Bildes wird durch Angabe des Blickwinkels und der Perspektive festgelegt.}, language = {de} } @misc{MelenkNeun1988, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Installation Guide for CRAY 1 / X-MP Systems Running UNICOS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4541}, number = {TR-88-03}, year = {1988}, abstract = {This guide describes the CRAY/UNICOS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running UNICOS. This document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, publication CP84.}, language = {en} } @misc{MelenkNeun1988, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE User s Guide for the CRAY 1 / CRAY X-MP Series Running UNICOS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4539}, number = {TR-88-02}, year = {1988}, abstract = {This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the Operating System UNICOS. The document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, (CP85).}, language = {en} } @misc{BuhtzBuhtz1988, author = {Buhtz, Rainer and Buhtz, Danuta Anna}, title = {TDLG 3.1 - Ein interaktives Programm zur Darstellung dreidimensionaler Modelle auf Rastergraphikger{\"a}ten.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4522}, number = {TR-88-01}, year = {1988}, abstract = {TDLG 3.1 dient zur Darstellung von dreidimensionalen Objekten, die sich aus offenen Linienz{\"u}gen, Dreieck- und Viereckelementen zusammensetzen. Dabei k{\"o}nnen verschiedene Visualisierungstechniken benutzt werden: Drahtmodell, Schattierung mit und ohne Lichtquelle, Hidden Surface Removal. Durch Verwendung von Konvertierungsprogrammen k{\"o}nnen auch IGES- und VDAFS- Dateien dargestellt werden.}, language = {de} } @misc{LangendorfPaetsch1987, author = {Langendorf, Jens and Paetsch, Olaf}, title = {GRAZIL (Graphical ZIB Language).}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4518}, number = {TR-87-07}, year = {1987}, abstract = {GRAZIL ist ein interaktives Programmpaket zur graphischen Darstellung von zwei-dimensionalen Kurvenverl{\"a}ufen. Dem Benutzer stehen zahlreiche Kommandos zum Gestalten des Layouts der Zeichnung zur Verf{\"u}gung. Die Eingabedaten m{\"u}ssen dem ZUGRIFF- Konzept gen{\"u}gen, wodurch die genaue Struktur der Daten erst zur Laufzeit bekannt sein muß und somit eine hohe Flexibilit{\"a}t und eine große Bandbreite der Einsatzm{\"o}glichkeiten erreicht wird. GRAZIL wurde mit der graphischen Grundsoftware BIZEPS2 und GKS entwickelt. Dadurch kann ein breites Rechner- und Ausgabeger{\"a}tespektrum genutzt werden.}, language = {de} } @misc{BuhtzLangendorfPaetschetal.1987, author = {Buhtz, Rainer and Langendorf, Jens and Paetsch, Olaf and Buhtz, Danuta Anna}, title = {ZUGRIFF - Eine vereinheitlichte Datenspezifikation f{\"u}r graphische Darstellungen und ihre graphische Aufbereitung.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4506}, number = {TR-87-06}, year = {1987}, abstract = {ZUGRIFF ist eine Dateischnittstelle f{\"u}r Graphikausgabe speziell numerischer Anwenderprogramme. Dieser Report beschreibt den Leistungsumfang der Spezifikation sowie die interaktive graphische Verarbeitung von ZUGRIFF- Dateien.}, language = {de} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Users Guide for the CRAY 1 / X-MP Series Running COS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4498}, number = {TR-87-05}, year = {1987}, abstract = {This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the CRAY Operating System (COS). The document was derived from the corresponding document for Vax/UNIX prepared by A.C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, (CP85).}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Installation Guide for CRAY 1 / X-MP Systems Running COS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4486}, number = {TR-87-04}, year = {1987}, abstract = {This guide describes the CRAY/COS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running COS. This document was derived from the corresponding document for Vax/Unix prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, publication CP84.}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {Portable Common LISP Subset Implementation for CRAY X+MP Computers.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4479}, number = {TR-87-03}, year = {1987}, abstract = {This document describes the installation procedure and maintenance for the Portable Common LISP Subset (PCLS) developed at the University of Utah.}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {Portable Standard LISP Implementation for CRAY X+MP Computers. Release of PSL 3.4 for COS.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4465}, number = {TR-87-02}, year = {1987}, abstract = {Portable Standard LISP (PSL) is a portable implementation of the programming language LISP constructed at the University of Utah. The version 3.4 of PSL was implemented for CRAY X-MP computers by Konrad Zuse-Zentrum Berlin; this implementation is based to an important part on the earlier implementation of PSL 3.2 at Salt Lake City, Los Alamos and Mendota Heights.}, language = {en} } @misc{BuschPoehleStech1987, author = {Busch, Hubert and P{\"o}hle, Uwe and Stech, Wolfgang}, title = {CRAY-Handbuch. - Einf{\"u}hrung in die Benutzung der CRAY.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4459}, number = {TR-87-01}, year = {1987}, abstract = {Das vorliegende Handbuch wendet sich an alle Benutzer des f{\"u}r den Norddeutschen Vektorrechnerverbund im ZIB installierten Rechners CRAY X-MP/24. Ein großer Teil der Darstellung ist der Optimierung von Programmen gewidmet, die in FORTRAN geschrieben sind. Gerade weil die CRAY einer der schnellsten Rechner der Welt ist, wird jeder Benutzer fr{\"u}her oder sp{\"a}ter selbst auf dieses Thema stoßen, denn die Maschine ist vornehmlich f{\"u}r Probleme bestimmt, die f{\"u}r die meisten anderen Rechner zu komplex sind. Maschinen der CRAY-Leistungsklasse beziehen einen erheblichen Teil ihrer Geschwindigkeit aus der parallelen Arbeit vieler Komponenten. Programme, die die jeweilige Architektur der Maschine ber{\"u}cksichtigen, k{\"o}nnen um Gr{\"o}ßenordnungen schneller (also wirtschaftlicher) sein als Programme, deren Autor beim Schreiben einen sogenannten "klassischen" Rechner vor seinem geistigen Auge hatte. Daher wird auch der technische Aufbau der CRAY X-MP im Handbuch erl{\"a}utert. Weitere Teile des Handbuches besch{\"a}ftigen sich mit den Vorrechnern und dem Rechnernetz.}, language = {de} } @misc{WitzigBeckenbachEifleretal.2016, author = {Witzig, Jakob and Beckenbach, Isabel and Eifler, Leon and Fackeldey, Konstantin and Gleixner, Ambros and Grever, Andreas and Weber, Marcus}, title = {Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes}, issn = {1438-0064}, doi = {10.1137/16M1091162}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60353}, year = {2016}, abstract = {In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.}, language = {en} } @misc{EhlkeRammLameckeretal.2013, author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Hege, Hans-Christian and Zachow, Stefan}, title = {Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41896}, year = {2013}, abstract = {We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.}, language = {en} } @misc{WinkelmannSchuettevonKleist2013, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1}, issn = {1438-0064}, doi = {10.4310/CMS.2014.v12.n5.a4}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41955}, year = {2013}, abstract = {Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodefficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs.}, language = {en} } @misc{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, issn = {1438-0064}, doi = {10.1145/2503210.2503254}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42187}, year = {2013}, abstract = {Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated.}, language = {en} } @misc{LieFackeldeyWeber2013, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A square root approximation of transition rates for a Markov State Model}, issn = {1438-0064}, doi = {10.1137/120899959}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42195}, year = {2013}, abstract = {Trajectory- or mesh-based methods for analyzing the dynamical behavior of large molecules tend to be impractical due to the curse of dimensionality - their computational cost increases exponentially with the size of the molecule. We propose a method to break the curse by a novel square root approximation of transition rates, Monte Carlo quadrature and a discretization approach based on solving linear programs. With randomly sampled points on the molecular energy landscape and randomly generated discretizations of the molecular configuration space as our initial data, we construct a matrix describing the transition rates between adjacent discretization regions. This transition rate matrix yields a Markov State Model of the molecular dynamics. We use Perron cluster analysis and coarse-graining techniques in order to identify metastable sets in configuration space and approximate the transition rates between the metastable sets. Application of our method to a simple energy landscape on a two-dimensional configuration space provides proof of concept and an example for which we compare the performance of different discretizations. We show that the computational cost of our method grows only polynomially with the size of the molecule. However, finding discretizations of higher-dimensional configuration spaces in which metastable sets can be identified remains a challenge.}, language = {en} } @misc{DresslerSteinke2013, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects}, issn = {1438-0064}, doi = {10.1007/978-3-642-54420-0_25}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42224}, year = {2013}, abstract = {Current programming models for heterogeneous devices with disjoint physical memory spaces require explicit allocation of device memory and explicit data transfers. While it is quite easy to manually implement these operations for linear data objects like arrays, this task becomes more difficult for non-linear objects, e.g. linked lists or multiple inherited classes. The difficulties arise due to dynamic memory requirements at run-time and the dependencies between data structures. In this paper we present a novel method to build a graph-based static data type description which is used to create code for injectable functions that automatically determine the memory footprint of data objects at run-time. Our approach is extensible to implement automatically generated optimized data transfers across physical memory spaces.}, language = {en} } @misc{RammMorilloVictoriaTodtetal.2013, author = {Ramm, Heiko and Morillo Victoria, Oscar Salvador and Todt, Ingo and Schirmacher, Hartmut and Ernst, Arneborg and Zachow, Stefan and Lamecker, Hans}, title = {Visual Support for Positioning Hearing Implants}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42495}, year = {2013}, abstract = {We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit.}, language = {en} } @misc{HombergBaumWiebeletal.2013, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42510}, year = {2013}, abstract = {An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.}, language = {en} }